Audit trail and exporting files in different formats from PipeBio

Audit trail, file tracking and exporting files with API

Company and product
September 20, 2021
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A dialogue showing how to download original source files from PipeBio bioinformatics platform

When data is uploaded to PipeBio, we parse it and display the results to users. Sequence and related data can then be exported in a wide range of common bioinformatic formats, such as .ab1, Genbank, Fasta, Fastq and more.

But what if you want the original, un-parsed file out? Many PipeBio customers require an audit trail of the sequences for taking drug candidates to clinical trials.

Exporting the originally uploaded files from PipeBio is easy via the online web application. Simply select the file to export, choose File > export from the menu and select “Source files” from the dropdown.

Downloading the source files of uploaded sequences on PipeBio
You are always able to download the source files for the uploaded sequences

These files might come from Sanger trace files (.ab1), Illumina NGS reads (fasta or fastq) or PacBio format.

You can also export these source files using the PipeBio REST API. A full working example with daily integration tests is available in the public PipeBio Github repo.

Here's how to download the original files from PipeBio Bioinformatics cloud in 3 steps:

1. Authenticate with PipeBio

[gist id=2ae466fa041559eca56ebe5ff6d8c80e]

2. Request a pre-signed url for the document you want to export

[gist id=2ae466fa041559eca56ebe5ff6d8c80e]

3. Download data from the pre-signed url

[gist id=2ae466fa041559eca56ebe5ff6d8c80e]


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